MUD transcript: 23-03-00
Course room(s): PPS
15:58:29 CharafB connects.
ClareS PPS HTTP 5m 45s 5m 27s
CharafB PPS HTTP 0s 0s
15:58:44 ClareS says "Hi"
15:58:52 CharafB says (to ClareS) "Hello, Clare"
15:59:05 ClareS says "I'd like to wait a couple of minutes before starting"
15:59:22 ClareS says "(I don't think it's even quite 16:00 yet)"
15:59:57 CharafB says "no problem... :)"
16:02:36 ClareS says "is your connection OK? Mine is rather slow"
16:02:37 ClareS says "(I don't think it's even quite 16:00 yet)"
16:04:42 SpyrosS connects.
ClareS PPS HTTP 11m 58s 1m 52s
CharafB PPS HTTP 6m 13s 4m 27s
SpyrosS PPS HTTP 0s 0s
16:04:42 CharafB says "mine seems ok... I hope!"
16:05:14 SpyrosS says "Hi everyone"
16:05:28 CharafB says (to Spir) "Hi"
16:05:31 ClareS says "Hi"
16:06:12 ClareS says "I guess we might as well start now... I am sure latecomers will join in OK"
16:06:26 ClareS says "how have you found the Molecular Forces section?"
16:07:43 CharafB says "It was really interesting but seemed very theoretical to me"
16:08:07 ClareS says "it is one of our hardest sections -- certainly the most mathematical"
16:08:56 CharafB says "Yes, it's seemes to be based on models extrapolating from little practical data"
16:09:08 SpyrosS says "Interesting. I felt at home with the maths, because of my physics background !"
16:09:27 ClareS says (to CharafB) "what do you mean exactly?"
16:10:49 ClareS says "the test of a molecular model is how well it can predict or reproduce a real structure"
16:11:08 CharafB says "I mean that the mathematical models to predict forces might be improved with time as data on 3D becomes greater, am I wrong?"
16:11:23 ClareS says "yes, of course"
16:11:56 ClareS says "but they haven't changed *very* much since structures were counted in hundreds rather than tens of thousands"
16:14:56 RamananS connects.
RamananS PPS Telnet 0s 0s
ClareS PPS HTTP 22m 12s 3m 0s
CharafB PPS HTTP 16m 27s 3m 48s
SpyrosS PPS HTTP 10m 14s 2m 38s
16:15:11 ClareS says (to RamananS) "Hi"
16:15:24 RamananS says "sorry I am late"
16:15:27 CharafB says "Hi"
16:15:38 ClareS says (to RamananS) "we are discussing the basis for mathematical modelling..."
16:15:38 RamananS says "hello"
16:15:48 SpyrosS says "Hi"
16:15:53 ClareS says (to RamananS) "don't worry about it!"
16:17:07 ClareS says "how are you finding this section?"
16:17:44 RamananS says "I did not get a chance to go through it all yet"
16:17:58 RamananS says "but very interesting"
16:18:18 ClareS says "it is quite a long section.. I might try to put on an extra MUD towards the end of next week if people would like one"
16:18:36 RamananS says "yes please"
16:18:51 ClareS says "have any of you any experience with molecular modelling?"
16:19:14 RamananS says "not me"
16:19:17 CharafB says "I found that we were going to the deepest aspect of chemistry which is in fact physics!"
16:19:46 ClareS says "Biophysics, perhaps..."
16:20:12 SpyrosS says "Yes, that's what I am trying to do at present."
16:20:37 RamananS says "should we know Coulomb's law upwards by heart for the exams"
16:20:42 ClareS says "what software are you using?"
16:20:52 CharafB says "I have no experience with modeling at all"
16:21:05 ClareS says (to RamananS) "if you *can*.. but it's much more important to know the basic principles"
16:21:25 PaulW connects.
RamananS PPS Telnet 6m 29s 48s
ClareS PPS HTTP 28m 41s 20s
CharafB PPS HTTP 22m 56s 33s
SpyrosS PPS HTTP 16m 43s 1m 13s
PaulW PPS HTTP 0s 0s
16:21:45 ClareS says (to PaulW) "Hi"
16:22:05 CharafB says "Hi Paul"
16:22:06 SpyrosS says "I have just started to use GROMACS for molecular dynamics and DELPHI for electrostatic calculations"
16:22:10 PaulW says "hello"
16:22:14 ClareS says "we don't attempt to teach modelling itself on this course"
16:22:36 ClareS says "we do give you a glimpse of the theory behind it"
16:22:53 ClareS says (to SpyrosS) "these are good academic programs but not the easiest to use"
16:22:59 SpyrosS says (to PaulW) "Hi"
16:24:37 PaulW says "Hi spyrosS"
16:24:55 CharafB says "I think it is important to know what are the laws regulating proteins interaction, which are resumed in the force field formula Etot =...."
16:25:08 SpyrosS says (to ClareS) "Exactly!!"
16:25:33 ClareS says (to CharafB) "can you paste in the URL so we can find the correct page quickly?"
16:25:36 CharafB says "But I don't see myself programming that kind modelling softwares!"
16:26:14 ClareS says (to SpyrosS) "there are two types of modelling program -- excellent programs written by academics that are cheap and difficult to use..."
16:26:36 ClareS says "...and commercial giant packages that are user-friendly but cost the earth"
16:26:38 CharafB says "http://pps9900.cryst.bbk.ac.uk/ppscore/section7/forcefield.html"
16:26:53 ClareS says "and, of course, visualisation tools like rasmol"
16:27:09 ClareS says "which to be pedantic make up a third class"
16:27:27 KevinO connects.
RamananS PPS Telnet 12m 31s 6m 50s
KevinO PPS Telnet 0s 0s
ClareS PPS HTTP 34m 43s 18s
CharafB PPS HTTP 28m 58s 49s
SpyrosS PPS HTTP 22m 45s 2m 19s
PaulW PPS HTTP 6m 2s 2m 50s
16:27:35 ClareS has found the equation...
16:29:38 AttilaR connects.
RamananS PPS Telnet 14m 42s 9m 1s
KevinO PPS Telnet 2m 11s 2m 11s
ClareS PPS HTTP 36m 54s 2m 3s
CharafB PPS HTTP 31m 9s 3m 0s
SpyrosS PPS HTTP 24m 56s 4m 30s
PaulW PPS HTTP 8m 13s 5m 1s
AttilaR PPS HTTP 0s 0s
16:29:52 ClareS says (to AttilaR) "Hi"
16:30:18 AttilaR says "Hello, sorry for being late!"
16:30:23 KevinO says "hi, sorry I'm late"
16:30:48 SpyrosS says "Hi"
16:30:59 CharafB says "Hi"
16:31:29 AttilaR says "What are we going to talk about this time?"
16:31:29 ClareS says "kevin & attila, we are looking at the force field equation: see http://pps9900.cryst.bbk.ac.uk/ppscore/section7/forcefield.html"
16:32:42 KevinO says (to ClareS) "got it"
16:32:57 ClareS says "a long time ago Charaf asked about the laws which regulated the interactions represented by the equation for Etot"
16:33:20 ClareS says (to CharafB) "can you expand further on what is puzzling you?"
16:33:51 CharafB says "I was wondering if we could Ee for errors accumulated in approximation of the partial forces"
16:34:15 CharafB says "sorry if we could ADD Ee"
16:34:40 AttilaR disconnects.
RamananS PPS Telnet 19m 44s 14m 3s
KevinO PPS Telnet 7m 13s 1m 58s
ClareS PPS HTTP 41m 56s 1m 20s
CharafB PPS HTTP 36m 11s 25s
SpyrosS PPS HTTP 29m 58s 3m 52s
PaulW PPS HTTP 13m 15s 10m 3s
16:35:03 ClareS says "it is very difficult to estimate such errors"
16:35:04 AttilaR connects.
RamananS PPS Telnet 20m 8s 14m 27s
KevinO PPS Telnet 7m 37s 2m 22s
ClareS PPS HTTP 42m 20s 1s
CharafB PPS HTTP 36m 35s 49s
SpyrosS PPS HTTP 30m 22s 4m 16s
PaulW PPS HTTP 13m 39s 10m 27s
AttilaR PPS HTTP 0s 0s
16:35:24 CharafB says "Models end up sometimes with puting to atoms exactly at the same place as mentionned somewhere in the ext about Van der Waals forces"
16:35:37 ClareS says "of course you always have to bear in mind that such an equation is an estimate"
16:35:56 VijayK connects.
RamananS PPS Telnet 21m 0s 15m 19s
KevinO PPS Telnet 8m 29s 3m 14s
ClareS PPS HTTP 43m 12s 19s
CharafB PPS HTTP 37m 27s 32s
SpyrosS PPS HTTP 31m 14s 5m 8s
PaulW PPS HTTP 14m 31s 11m 19s
AttilaR PPS HTTP 52s 52s
VijayK PPS HTTP 0s 0s
16:36:01 AttilaR says "Sorry, there hase been some problem with the connection."
16:36:12 CharafB says "This implies that some approximation errors are greater than expected"
16:36:26 ClareS says "if you wanted to be exactly accurate you would have to use quantum mechanics, and that is *impossible* for large molecules like proteins"
16:36:33 VijayK says "I have just got in sorry for being late"
16:37:05 ClareS says "it is quite surprising that molecular mechanics often gives such reasonable results"
16:37:22 ClareS says (to VijayK) "don't worry..."
16:39:00 CharafB says "Oh yes, of course, I am absolutely astonished by what we can make already but it's seems like there is ground for improvement which is great!"
16:39:09 VijayK says "Iam not familiar with this - molecular mechanics"
16:39:14 ClareS says "there is certainly ground for improvement..."
16:39:47 ClareS says (to VijayK) "molecular mechanics is the term used for modelling molecules using classical (not quantum) mechanics"
16:40:21 ClareS says "i.e. with "balls" and "sticks", bond lengths and angles rather than molecular orbitals"
16:40:30 VijayK says "Eaxmples of classical mechanics used commonly"
16:40:58 ClareS says "all the equations given in these section are classical mechanics equations"
16:41:27 VijayK says "Shall we be dealing with quantum mechanics in this course?"
16:41:27 CharafB says "No electron spin, then! ;)"
16:42:00 RamananS says "are 'optimum bond lengths' and equilibrium bond lengths as in the bond sterching analysis the same?"
16:42:17 CharafB says "I have a simple query on page:"
16:42:21 CharafB says "http://pps9900.cryst.bbk.ac.uk/ppscore/section7/helix3.html"
16:42:32 ClareS says "no electron spin -- and no quantum mechanics in this course"
16:42:50 AttilaR says "I think sometimes it is very good to make understand things with these classical terms and equations, because they are more easily understood by me."
16:42:57 ClareS says "and yes, optimum bond lengths & equilibrium bond lengths are the same"
16:43:11 CharafB says "How is caculated the dipole moment?"
16:43:51 ClareS says "equilibrium bond length is in some ways a moer accurate term because it implies that bonds are not actually fixed rods"
16:45:17 ClareS says "I am not exactly sure how the dipole moment is calculated"
16:46:11 CharafB says "Would you know what is the unit... D doesn't ring a bell to me..."
16:46:45 ClareS says "it's based on the separation of partial charges on atoms but I don't know the maths"
16:46:57 ClareS says "charge divided by distance"
16:47:42 VijayK says "Regarding the section on Programs for Modelling - how much of it will be useful in this course?"
16:48:24 ClareS says "you don't *need* to use any of these programs to pass the course"
16:48:47 ClareS says "that section is included out of interest to give pointers to people who want to take the subject further"
16:48:58 VijayK says "Thanks it is good to know"
16:49:10 ClareS says "of course, some people do use modelling in their projects and that's OK but they don't have to"
16:49:21 RamananS says "in ....helix3.html the examples at the end , are they all hypothetical or known interactions ()[D"
16:50:07 ClareS says (to RamananS) "they are known interactions"
16:51:01 ClareS says "you can see this easiest if you look at the ligand - protein interactions in flavodoxin & lactate dehydrogenase"
16:51:46 ClareS says "e.g. in flavodoxin a negatively charged phosphate group in the ligand binds to..."
16:52:18 ClareS says "... the amino terminus of an alpha helix, which is slightly positively charged"
16:52:57 RamananS says "is it not half a unit charge not 'slight'?"
16:53:02 ClareS says "is that clear?"
16:53:18 ClareS says "less than a single electron..."
16:53:48 RamananS says "things are definitely clearer , I'll take a look again..."
16:54:13 VijayK says "In the section Hydrogen Bonds II, Iam a little puzzled by the terms CG-OD, CD-OE, CZ and NZ etc"
16:55:20 ClareS says (to VijayK) "they are shortened forms for particular side chain atoms and bonds"
16:55:32 KevinO says "on Dipole moments, the unit (D) is Debye and a reference to them is http://www.dartmouth.edu/artsci/chem/introchem/dipole.html"
16:55:47 ClareS says "e.g. CG-OD is a bond between a gamma-carbon atom and a delta-oxygen atom"
16:55:53 RamananS says "thanks Kev"
16:56:10 CharafB says (to KevinO) "Thanks!"
16:56:12 ClareS says (to KevinO) "Thanks -- I'd forgotten the name of the unit. Sorry..."
16:57:23 ClareS says "that URL gives a very clear description of the dipole moment defined as charge * distance"
16:58:24 VijayK says "Thanks again. Also thanks for the URL on dipole moment"""
16:59:01 ClareS is looking for an archived image of flavodoxin showing the interaction
17:00:12 CharafB says "Would anyone know a link to a quick refresher URL on thermodynamics, I studied enthalpy and entropy 10 years ago on 1st year at the vet school, it seems so far away!"
17:01:05 ClareS says "For flavodoxin: see http://www.biochem.ucl.ac.uk/bsm/pdbsum/2fdx/main.html"
17:01:18 ClareS says "that is an entry in the PDBsum database"
17:02:27 RamananS says "for thermodyn... try google.com with correct spelling and word 'y...."
17:02:27 ClareS says "if you follow the link to LIGPLOT you will see the negatively charged phosphate group binding to residues 7,8,9 and 12"
17:02:52 ClareS says "you will also see that those residues are at the N terminus of an alpha helix"
17:04:36 CharafB says (to RamananS) "Thanks very much, Ramanan!"
17:04:57 ClareS tried it and found a lot of books on the subject
17:06:25 ClareS says "Try Basic Chemical Thermodynamics: http://orac.sunderland.ac.uk/~hs0bcl/td1.htm"
17:08:22 ClareS says "that seems, at first glance, to be accessible and quite mathematical enough for this course"
17:08:51 CharafB says (to ClareS) "This looks great ... Thanks!"
17:10:32 ClareS says "nothing on entropy & the second law, tho' unfortunately"
17:11:14 ClareS says "I'd like to close the meeting quite soon: are there any more questions or points for discussion?"
17:11:48 KevinO says "not from me"
17:12:05 RamananS says "is ther e going to be a more MUD sessions on this section?"
17:12:30 AttilaR says "I think I have to go now."
17:13:35 VijayK says "Section 7 was great. but I have all the relevant sections on protein geometry etc to get the impact"
17:14:31 SpyrosS says "I have to go too, bye everyone"
17:14:38 KevinO says "'bye - lunch time!"
17:14:57 AttilaR disconnects.
RamananS PPS Telnet 1h 0m 2m 52s
KevinO Common Telnet 47m 30s 0s
ClareS PPS HTTP 1h 22m 3m 43s
CharafB PPS HTTP 1h 16m 6m 6s
SpyrosS PPS HTTP 1h 10m 26s
PaulW PPS HTTP 53m 32s 50m 20s
VijayK PPS HTTP 39m 1s 1m 22s
17:15:09 ClareS says (to VijayK) "there is more info on the names given to atoms in protein side chains at http://pps9900.cryst.bbk.ac.uk/ppscore/section3/jonc/conform.html"
17:15:10 KevinO disconnects.
RamananS PPS Telnet 1h 0m 3m 5s
ClareS PPS HTTP 1h 22m 1s
CharafB PPS HTTP 1h 16m 6m 19s
SpyrosS PPS HTTP 1h 10m 39s
PaulW PPS HTTP 53m 45s 50m 33s
VijayK PPS HTTP 39m 14s 1m 35s
17:15:18 ClareS says "(in section 3)"
17:15:33 VijayK says "Thank you"
17:15:38 ClareS says "don't forget the session to-morrow at 23:00"
17:15:41 AttilaR connects.
RamananS PPS Telnet 1h 0m 3m 36s
ClareS PPS HTTP 1h 22m 3s
CharafB PPS HTTP 1h 17m 6m 50s
SpyrosS PPS HTTP 1h 10m 1m 10s
PaulW PPS HTTP 54m 16s 51m 4s
AttilaR PPS HTTP 0s 0s
VijayK PPS HTTP 39m 45s 8s
17:15:48 CharafB says "I would agree with Vijay, that's the basis for the rest"
17:16:32 SpyrosS disconnects.
RamananS PPS Telnet 1h 1m 4m 27s
ClareS PPS HTTP 1h 23m 36s
CharafB PPS HTTP 1h 18m 44s
PaulW PPS HTTP 55m 7s 51m 55s
AttilaR PPS HTTP 51s 51s
VijayK PPS HTTP 40m 36s 59s
17:16:38 ClareS says "... and remember that British Summer Time starts next week. I will still give MUD times in GMT but the time in the UK will be different"
17:17:11 AttilaR says "Good bye everybody!"
17:17:28 AttilaR disconnects.
RamananS PPS Telnet 1h 2m 5m 23s
ClareS PPS HTTP 1h 24m 50s
CharafB PPS HTTP 1h 18m 1m 40s
PaulW PPS HTTP 56m 3s 52m 51s
VijayK PPS HTTP 41m 32s 1m 55s
17:17:36 CharafB says (to AttilaR) "Bye!"